Unde venis? Bacterial resistance from environmental reservoirs to lettuce: tracking microbiome and resistome over a growth period.

Fresh produce is suggested to contribute highly to shaping the gut resistome. We investigated the impact of pig manure and irrigation water quality on microbiome and resistome of field-grown lettuce over an entire growth period. Lettuce was grown under four regimes, combining soil amendment with manure (with/without) with sprinkler irrigation using river water with an upstream wastewater input, disinfected by UV (with/without).

Minimally destructive hDNA extraction method for retrospective genetics of pinned historical Lepidoptera specimens.

The millions of specimens stored in entomological collections provide a unique opportunity to study historical insect diversity. Current technologies allow to sequence entire genomes of historical specimens and estimate past genetic diversity of present-day endangered species, advancing our understanding of anthropogenic impact on genetic diversity and enabling the implementation of conservation strategies. A limiting challenge is the extraction of historical DNA (hDNA) of adequate quality for sequencing platforms.

Clonal genomic population structure of Beauveria brongniartii and Beauveria pseudobassiana: Pathogens of the common European cockchafer (Melolontha melolontha L.).

Beauveria brongniartii is a fungal pathogen that infects the beetle Melolontha melolontha, a significant agricultural pest in Europe. While research has primarily focused on the use of B. brongniartii for controlling M.

Spatial and temporal patterns in the population genomics of the European cockchafer in the Alpine region.

The European cockchafer is an agricultural pest in many European countries. Populations have a synchronized 3 or 4 years life cycle, leading to temporally isolated populations. Despite the economic importance and availability of comprehensive historical as well as current records on cockchafer occurrence, population genomic analyses of are missing.

relative abundance in shower hose biofilms is associated with specific microbiome members.

are natural inhabitants of building plumbing biofilms, where interactions with other microorganisms influence their survival, proliferation, and death. Here, we investigated the associations of with bacterial and eukaryotic microbiomes in biofilm samples extracted from 85 shower hoses of a multiunit residential building. spp.

Water column dynamics control nitrite-dependent anaerobic methane oxidation by Candidatus "Methylomirabilis" in stratified lake basins.

We investigated microbial methane oxidation in the water column of two connected but hydrodynamically contrasting basins of Lake Lugano, Switzerland. Both basins accumulate large amounts of methane in the water column below their chemoclines, but methane oxidation efficiently prevents methane from reaching surface waters. Here we show that in the meromictic North Basin water column, a substantial fraction of methane was eliminated through anaerobic methane oxidation (AOM) coupled to nitrite reduction by Candidatus Methylomirabilis.

Infection by a eukaryotic gut parasite in wild Daphnia sp. associates with a distinct bacterial community.

Host-associated bacterial communities play an important role in host fitness and resistance to diseases. Yet, few studies have investigated tripartite interaction between a host, parasite and host-associated bacterial communities in natural settings. Here, we use 16S rRNA gene amplicon sequencing to compare gut- and body- bacterial communities of wild water fleas belonging to the Daphnia longispina complex, between uninfected hosts and those infected with the common and virulent eukaryotic gut parasite Caullerya mesnili (Family: Ichthyosporea).

A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae).

Understanding the genetic changes associated with the evolution of biological diversity is of fundamental interest to molecular ecologists. The assessment of genetic variation at hundreds or thousands of unlinked genetic loci forms a sound basis to address questions ranging from micro- to macroevolutionary timescales, and is now possible thanks to advances in sequencing technology. Major difficulties are associated with (i) the lack of genomic resources for many taxa, especially from tropical biodiversity hotspots; (ii) scaling the numbers of individuals analysed and loci sequenced; and (iii) building tools for reproducible bioinformatic analyses of such data sets.

Spatio-temporal patterns of multi-trophic biodiversity and food-web characteristics uncovered across a river catchment using environmental DNA.

Accurate characterisation of ecological communities with respect to their biodiversity and food-web structure is essential for conservation. However, combined empirical study of biodiversity and multi-trophic food webs at a large spatial and temporal resolution has been prohibited by the lack of appropriate access to such data from natural systems. Here, we assessed biodiversity and food-web characteristics across a 700 km riverine network over seasons using environmental DNA.

Species ecology explains the spatial components of genetic diversity in tropical reef fishes.

Generating genomic data for 19 tropical reef fish species of the Western Indian Ocean, we investigate how species ecology influences genetic diversity patterns from local to regional scales. We distinguish between the , and components of genetic diversity, which we subsequently link to six ecological traits. We find that the and components of genetic diversity are strongly correlated so that species with a high total regional genetic diversity display systematically high local diversity.

Transcriptome-wide SNPs for Botrychium lunaria ferns enable fine-grained analysis of ploidy and population structure.

Ferns are the second most diverse group of land plants after angiosperms. Extant species occupy a wide range of habitats and contribute significantly to ecosystem functioning. Despite the importance of ferns, most taxa are poorly covered by genomic resources and within-species studies based on high-resolution markers are entirely lacking.

Transcriptome profiling of Lymnaea stagnalis (Gastropoda) for ecoimmunological research.

Background: Host immune function can contribute to numerous ecological/evolutionary processes. Ecoimmunological studies, however, typically use one/few phenotypic immune assays and thus do not consider the complexity of the immune system. Therefore, "omics" resources that allow quantifying immune activity across multiple pathways are needed for ecoimmunological models.

Dioecy Is Associated with High Genetic Diversity and Adaptation Rates in the Plant Genus Silene.

About 15,000 angiosperm species (∼6%) have separate sexes, a phenomenon known as dioecy. Why dioecious taxa are so rare is still an open question. Early work reported lower species richness in dioecious compared with nondioecious sister clades, raising the hypothesis that dioecy may be an evolutionary dead-end.

A de novo chromosome-level genome assembly of Coregonus sp. "Balchen": One representative of the Swiss Alpine whitefish radiation.

Salmonids are of particular interest to evolutionary biologists due to their incredible diversity of life-history strategies and the speed at which many salmonid species have diversified. In Switzerland alone, over 30 species of Alpine whitefish from the subfamily Coregoninae have evolved since the last glacial maximum, with species exhibiting a diverse range of morphological and behavioural phenotypes. This, combined with the whole genome duplication which occurred in the ancestor of all salmonids, makes the Alpine whitefish radiation a particularly interesting system in which to study the genetic basis of adaptation and speciation and the impacts of ploidy changes and subsequent rediploidization on genome evolution.

Disentangling the effects of geographic peripherality and habitat suitability on neutral and adaptive genetic variation in Swiss stone pine.

It is generally accepted that the spatial distribution of neutral genetic diversity within a species' native range mostly depends on effective population size, demographic history, and geographic position. However, it is unclear how genetic diversity at adaptive loci correlates with geographic peripherality or with habitat suitability within the ecological niche. Using exome-wide genomic data and distribution maps of the Alpine range, we first tested whether geographic peripherality correlates with four measures of population genetic diversity at > 17,000 SNP loci in 24 Alpine populations (480 individuals) of Swiss stone pine (Pinus cembra) from Switzerland.

The genetic mechanism of selfishness and altruism in parent-offspring coadaptation.

The social bond between parents and offspring is characterized by coadaptation and balance between altruistic and selfish tendencies. However, its underlying genetic mechanism remains poorly understood. Using transcriptomic screens in the subsocial European earwig, , we found the expression of more than 1600 genes associated with experimentally manipulated parenting.

Small-Scale Heterogeneity in Drinking Water Biofilms.

Biofilm heterogeneity has been characterized on various scales for both natural and engineered ecosystems. This heterogeneity has been attributed to spatial differences in environmental factors. Understanding their impact on localized biofilm heterogeneity in building plumbing systems is important for both management and representative sampling strategies.

Population genomic evidence for plant glacial survival in Scandinavia.

Quaternary glaciations have played a major role in shaping the genetic diversity and distribution of plant species. Strong palaeoecological and genetic evidence supports a postglacial recolonization of most plant species to northern Europe from southern, eastern and even western glacial refugia. Although highly controversial, the existence of small in situ glacial refugia in northern Europe has recently gained molecular support.

Genomic imprinting mediates dosage compensation in a young plant XY system.

Sex chromosomes have repeatedly evolved from a pair of autosomes. Consequently, X and Y chromosomes initially have similar gene content, but ongoing Y degeneration leads to reduced expression and eventual loss of Y genes. The resulting imbalance in gene expression between Y genes and the rest of the genome is expected to reduce male fitness, especially when protein networks have components from both autosomes and sex chromosomes.

Has adaptation occurred in males and females since separate sexes evolved in the plant ?

The evolution of separate sexes may involve changed expression of many genes, as each sex adapts to its new state. Evidence is accumulating for sex differences in expression even in organisms that have recently evolved separate sexes from hermaphrodite or monoecious (cosexual) ancestors, such as some dioecious flowering plants. We describe evidence that a dioecious plant species with recently evolved dioecy, , has undergone adaptive changes that improve functioning in females, in addition to changes that are probably pleiotropic effects of male sterility.

Temporal dynamics of microbiota before and after host death.

The habitats that animals, humans and plants provide for microbial communities are inevitably transient, changing drastically when these hosts die. Because microbes associated with living hosts are ensured prime access to the deceased host's organic matter, it is feasible that opportunistic, adaptable lifestyles are widespread among host-associated microbes. Here we investigate the temporal dynamics of microbiota by starving to death a host-the planktonic Crustacean Daphnia magna-and tracking the changes in its microbial community as it approaches death, dies and decomposes.

Genomewide signatures of selection in Epichloë reveal candidate genes for host specialization.

Host specialization is a key process in ecological divergence and speciation of plant-associated fungi. The underlying determinants of host specialization are generally poorly understood, especially in endophytes, which constitute one of the most abundant components of the plant microbiome. We addressed the genetic basis of host specialization in two sympatric subspecies of grass-endophytic fungi from the Epichloë typhina complex: subsp.

Phylogenetic clustering of small low nucleic acid-content bacteria across diverse freshwater ecosystems.

Here we used flow cytometry (FCM) and filtration paired with amplicon sequencing to determine the abundance and composition of small low nucleic acid (LNA)-content bacteria in a variety of freshwater ecosystems. We found that FCM clusters associated with LNA-content bacteria were ubiquitous across several ecosystems, varying from 50 to 90% of aquatic bacteria. Using filter-size separation, we separated small LNA-content bacteria (passing 0.

The genomes of Crithidia bombi and C. expoeki, common parasites of bumblebees.

Trypanosomatids (Trypanosomatidae, Kinetoplastida) are flagellated protozoa containing many parasites of medical or agricultural importance. Among those, Crithidia bombi and C. expoeki, are common parasites in bumble bees around the world, and phylogenetically close to Leishmania and Leptomonas.